Align L-piperidine-6-carboxylate dehydrogenase; EC 1.2.1.21 (characterized, see rationale)
to candidate 5210745 Shew_3173 succinic semialdehyde dehydrogenase (RefSeq)
Query= uniprot:Q88CC3 (496 letters) >FitnessBrowser__PV4:5210745 Length = 485 Score = 192 bits (489), Expect = 2e-53 Identities = 144/462 (31%), Positives = 219/462 (47%), Gaps = 23/462 (4%) Query: 21 YPVHTPIDGSQIASVKLLGKAETIARIDQAQSAFEAWRSVPAPRRGELVRLFGEVLREHK 80 + V P IA V +T I A+ A W A R L+R + ++ EH+ Sbjct: 27 FDVVNPASQEVIAQVVDASLDDTQEAILAAKRALPEWSKRSANERAALMRKWFNLMMEHQ 86 Query: 81 ADLGELVSIEAGKITQEGLGEVQEMIDICDFAVGLSRQLYGLTIASERPGHHMRETWHPL 140 DLG L+++E GK E GE+ D+ +++YG TI + + P+ Sbjct: 87 EDLGRLLTLEQGKPLAEAKGEIAYGAAFIDWFAEEGKRVYGDTIPAPANDKRILVIKQPV 146 Query: 141 GVVGVISAFNFPVAVWAWNTALALVAGNSVVWKPSEKTPLTALACQALFEKALKAFGDAP 200 GVV I+ +NFP A+ A A AL AG + V +PS TPL+ALA L E+A P Sbjct: 147 GVVASITPWNFPNAMIARKAAAALAAGCTFVARPSPLTPLSALAMAELAERA-----GIP 201 Query: 201 AGLAQLVIGGREA--GEAMVDDPRVPLVSATGSTRMGREVGPRVAARFGRSILELGGNNA 258 AG+ +V+G G+ + P V + TGST +G+ + + A + +ELGGN Sbjct: 202 AGVFNIVVGEDAVGMGKVLTQHPDVAKFTFTGSTAVGKILLAQCATSVKKVSMELGGNAP 261 Query: 259 MILAPSADLDLAVRGILFSAVGTAGQRCTTLRRLIVHRSIKDEVVARVKAAYGKVRIGDP 318 I+ AD+D AV+G L S AGQ C R+ V + + + AA +++GD Sbjct: 262 FIVFDDADIDAAVQGALISKYRNAGQTCVCTNRIFVQKGVAAAFTEKFTAAVANLKLGDG 321 Query: 319 RKDNL-VGPLIDKQSFDAMQGALAKARDEGGQ----VFGGE-RQLADQYPNAYYVSPAIA 372 D + VGP+I K DA+Q L D V GG+ +L + + V+ Sbjct: 322 LGDGVTVGPMISK---DAVQNVLKLVDDTVASGAKLVTGGQPSELGESFLAPVIVTDVTN 378 Query: 373 EMPAQSDVVRHETFAPILYVLAYDDFEEALRLNNEVPQGLSSCIFTTDIREAERFQSASG 432 EMP + R+E F P+ ++++D EAL + N+ GL++ + DI F+ A G Sbjct: 379 EMP----LARNEIFGPVTPIISFDSEAEALAMANDTEYGLAAYFYARDI--GRIFRVAEG 432 Query: 433 SDCGIANVNIGTSGAEIGGAFGGEKETGGGRESGSDAWKGYM 474 + G+ VN G + FGG K++G GRE Y+ Sbjct: 433 LEYGMVGVNEGII-SNAAAPFGGVKQSGNGREGSKYGLDDYL 473 Lambda K H 0.318 0.135 0.396 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 536 Number of extensions: 29 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 496 Length of database: 485 Length adjustment: 34 Effective length of query: 462 Effective length of database: 451 Effective search space: 208362 Effective search space used: 208362 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory